npSeq is an R package for the significance analysis of sequencing data. The statistic used by npSeq is exactly the same as that in SAM 4.0. The only difference is that npSeq uses symmetric cutoffs, while SAM uses asymmetric cutoffs. Therefore, for some datasets, all significant genes obtained by SAM are either all up-regulated or all down-regulated, but npSeq almost always gives significant genes that include both up-regulated genes and down-regulated genes.
- MacOsX/ Linux / WIndows
- R Package
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Jun Li and Robert Tibshirani (2011)
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
Stat Methods Med Res. 2011 Nov 28.